Protesters stand in solidarity with rape victims on the campus of Brigham Young University during a sexual assault awareness demonstration on April 20.

Rick Bowmer/AP

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Madi Barney, a sophomore at Brigham Young University, says she was raped in her off-campus apartment last September by an older man. Provo, Utah, prosecutors are pursuing a case against the individual.

But rather than focus on the plight of a young assault victim, BYU officials contacted Ms. Barney after receiving a police report with something else on their minds: that it looked like she had violated the school’s honor code.

BYU’s honor code, which every student must sign, is long and complex, banning students from coffee, premarital sex, and even hanging out in a bedroom with someone of the opposite sex. It’s not known what part of the code Barney allegedly broke to warrant academic punishment. She has said she’s struggled with classes after her ordeal. Now she feels twice victimized.

Barney on Monday filed a discrimination complaint with the United States Office of Civil Rights, claiming that the Mormon university failed to extend services she should receive under Title IX protections from discrimination. She also started a petition urging the university to make sexual assault victims immune from honor code punishments. It has nearly 100,000 signatures.

BYU spokeswoman Carrie Jenkins told the Salt Lake City Tribune this week that the school is “going to be looking at changes” to its honor code policy around the issue of rape.

The debate at BYU dovetails into broader cultural and legal shifts that are forcing colleges and universities to confront the wrenching toll of campus rapes, and especially how to assure victims that they will not be punished for coming forward with their stories.

In this case, the issue comes down to "the letter of the law" versus the "spirit of the law," says Ryan Cragun, a sociologist who specializes in Mormonism at the University of Tampa.

“For the [BYU] administration, the honor code is separate in their minds from the crime that happened: In other words, she’s not at fault for rape, but she is at fault for being sexually intimate,” he says. “But for a lot of people, blaming and shaming the victim is a total validation of rape culture.”

The plight of assaulted women needs to be taken more seriously, experts say. In the BYU situation, that may extend to examining the unintended effects of enforcing the honor code.

“Norms around violence are embedded in everyday actions and attitudes,” says Vicky Banyard, a sociologist at the University of New Hampshire in Durham. “And until we’re willing to look at all of those, we are not going to fully deal with the whole scope of this problem.”

BYU officials have said that a sexual assault report doesn’t automatically lead to an honor-code investigation. But at a recent conference, one BYU dean said the school “doesn’t apologize” for referring some such cases to the school’s honor code committee if there’s evidence of someone breaking the religious covenant.

The church sees that policy as part of its mission to provide spiritual guidance to young people. But critics say the overall harm may be greater, since the tack appears to punish victims and empower perpetrators.

“BYU is genuine when it says that a student would never be referred to the honor code office for being a victim of sexual assault,’” the Salt Lake City Tribune’s editorial board wrote this week. “But it still is enabling perpetrators ... by setting up a barrier to student victims coming forward.”

Though it's difficult to determine the exact breadth of the problem of a "rape culture" on campus, as many as 1 in 5 college women have reported in surveys to being victims of some form of sexual assault. According to a Department of Justice report, only about 5 percent of assaults are reported, in part, because victims worry how their allegations will be treated by university officials. Others cite a discredited report by Rolling Stone about the University of Virginia last year as evidence that "rape culture" is overblown as a force on US campuses.

For its part, the Obama administration has issued several controversial memos urging schools to better protect those who report sexual assault in order to curb the frequency of attacks on campus.

"Highlighting the absolute necessity of effective prevention, that's the message that has started to come out more and more over the last couple of years," says Ms. Banyard.

Honor codes are part of American educational tradition, a way to focus college students, many who are on their own for the first time in their lives, on the value of good citizenship and honesty. The point is to establish ethical principles that bind students together – and also make them liable, usually through some form of academic punishment, if rules are broken.

The first honor code dates back to 1736, adopted by the College of William and Mary. Guilford College has distilled its code into a single line: “I have been honest and observed no dishonesty.”

As a church-run university – and a huge one at 30,000 students – the choices facing BYU may be particularly challenging.

“They’re going to try to find a way to walk a line that’s super-fine,” says Mr. Cragun. “They’re likely to say, ‘We will try and side with the victim as much as possible.’ ” But “I don’t know that they can back away completely” from honor code rules banning premarital sex.